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lit-review-topic-12

Lit review topic 12: HPRC v1 v2 population pangenomes

Metadata

Statusdone
Assignedagent-925
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Modelclaude:sonnet
Created2026-05-06T01:46:50.197289117+00:00
Started2026-05-06T13:34:23.060331913+00:00
Completed2026-05-06T13:46:30.218995837+00:00
Tagslit-review, eval-scheduled
Tokens108991 in / 1284 out
Eval score0.03
└ blocking impact0.00
└ completeness0.05
└ constraint fidelity0.55
└ coordination overhead0.10
└ correctness0.00
└ downstream usability0.00
└ efficiency0.10
└ intent fidelity0.00
└ style adherence0.00

Description

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LIT-REVIEW TOPIC TASK — READ THIS PREAMBLE BEFORE ANYTHING ELSE

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PRIOR-RUN FAILURE WARNING.

In the previous fanout, 12 of 14 agents reported wg done in 30-60s

WITHOUT writing or committing any output file. Their evaluation scores

ranged 0.02-0.17. They cached the brief, generated ~1.6k tokens of

output (probably just a "plan"), and exited. DO NOT BE THAT AGENT.

YOUR JOB IS TO PRODUCE TWO COMMITTED FILES, NOT A PLAN TO PRODUCE THEM.

The deliverables are file content on disk. If you have not written

1500+ words to the .md file and 10+ entries to the .bib file, you are

not done — regardless of how thoroughly you have "thought about" the

topic.

REQUIRED STEP ORDER. Do these in this exact sequence:

STEP 1 — orient (~3 min):

- Read paper_prep/synthesis/ABSTRACT_nature.md (if present) or

ABSTRACT_BoG.md (fallback). This is the canonical anchor.

- Read paper_prep/synthesis/CROSSWALK.md sections 1-3 to find which

claims (C1-C8) your topic supports.

- Read end-to-end-report/report/12_literature.md (Andrea's literature

confirmation table) — your seed references probably appear there.

- Run wg log <your-task-id> "Step 1 done — substrate read".

STEP 2 — search (~10 min):

- Use WebSearch to find 10-30 relevant papers for THIS TOPIC's scope

(see THIS-TOPIC block below). Search PubMed, Google Scholar,

biorxiv, Nature/Cell/Science archives. For each candidate paper,

capture: author, year, title, journal, DOI/URL, 1-sentence

relevance to your topic.

- You may also use WebFetch to read a paper's abstract or full text

if a search hit looks central.

- Run wg log <your-task-id> "Step 2 done — found N papers" where N

is your candidate count.

STEP 3 — write the .md file (~20 min):

- File: paper_prep/lit_review/topic_NN_.md (NN = your topic

number; slug = your topic's hyphenated short name)

- Required structure (5 sections, ~300 words each = ~1500 words

total minimum):

## Era overview (~300 words)

When did this topic emerge as a research area? What questions

drove early work?

## Key papers in chronological order (~300 words)

Walk through 5-10 milestone references with 2-3 sentences each

explaining what each paper established.

## Findings most relevant to claim Cn of the abstract (~300 words)

Which abstract claim(s) does this topic anchor? What specific

papers provide the strongest support? What is contested?

## How this topic intersects adjacent topics (~300 words)

Brief: where does this topic touch the other topics in this

fanout? Surface 2-3 cross-references.

## Open questions and recent developments (~300 words)

What's still unsettled? What 2020-2026 papers have shifted

thinking?

- You may go LONGER per section if you have material; the floor is

~1500 words total.

- Cite references inline using \cite{key} or [Author Year] style;

the .bib file (next step) will provide the lookup.

- Run wg log <your-task-id> "Step 3 done — wrote N words" where N

is your wc -w count.

STEP 4 — write the .bib file (~5 min):

- File: paper_prep/lit_review/topic_NN_.bib

- One BibTeX entry per reference cited in your .md. Use your topic's

slug as a key prefix to avoid collisions: e.g. for topic 05

acrocentric, keys like @article{guarracino2023acrocentric,...}.

- REQUIRED FIELDS per entry: author, title, year, journal/booktitle,

and either doi or url.

- Minimum 10 entries.

- DO NOT duplicate entries already in paper_prep/synthesis/REFERENCES.bib —

run grep -E "^@" paper_prep/synthesis/REFERENCES.bib to see the

existing keys before you start writing.

- Run wg log <your-task-id> "Step 4 done — wrote N entries" where

N is your entry count.

STEP 5 — verify on disk (~1 min):

- Run these commands and confirm each:

ls -la paper_prep/lit_review/topic_*.md # your .md exists

ls -la paper_prep/lit_review/topic_*.bib # your .bib exists

wc -w paper_prep/lit_review/topic_*.md # >= 1500

grep -c "^@" paper_prep/lit_review/topic_*.bib # >= 10

- If ANY of these checks fails, go back to step 3 or 4. DO NOT

PROCEED to step 6 until all four checks pass.

STEP 6 — commit + push (~1 min):

- git add paper_prep/lit_review/topic_NN_.md paper_prep/lit_review/topic_NN_.bib

- git commit -m "docs: lit review topic NN — "

- The harness handles push.

- Run wg log <your-task-id> "Step 6 done — committed <hash>".

STEP 7 — record artifacts and call wg done:

- wg artifact paper_prep/lit_review/topic_NN_*.md

- wg artifact paper_prep/lit_review/topic_NN_*.bib

- wg done

DO NOT call wg done before Step 6 has committed both files. The

harness will not stop you, but the evaluator WILL flag it (the prior

round's failed agents got 0.02-0.17). Verify with Step 5 first.

IF YOU ARE STUCK, do NOT call wg done to escape — call

wg log <your-task-id> "stuck on <step>: <specific issue>" and fail

explicitly with wg fail <your-task-id> "<reason>" so a human can

triage.

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THIS TOPIC (12 — slug: hprc_population_pangenomes): The Human Pangenome Reference Consortium — Liao 2023 HPRC v1 (47 diploids); HPRC v2 (this manuscript's companion paper, 466 haplotypes). Earlier population pangenome efforts: 1000 Genomes structural variants, gnomAD-SV, HGDP. Why HPRC v2 enables this paper specifically. Lineage of pangenome reference construction. TIME RANGE: 2010-present (1000 Genomes era through HPRC v2). SEED REFERENCES: Liao 2023 HPRC v1; 1000 Genomes Project structural variant papers (Sudmant 2015 etc.); HPRC v2 (cite as "in submission" / preprint if available — search biorxiv 2026). Find ~10-20 more on population pangenomics, reference-free assembly approaches, pangenome reference construction. Anchor claim(s) per CROSSWALK: C1 (HPRC v2 companion framing), C3 (466-haplotype dataset).

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RE-DISPATCH NOTE (claude:sonnet, 2026-05-06)

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This task has been redispatched from codex:gpt-5.5 (which had ~14-50%

engagement on these tasks — see ~/.claude/projects/-moosefs-erikg-phrs/memory/

feedback_codex_gpt55_lazy_execution.md for the full incident report).

When you start, you may see:

- paper_prep/lit_review/topic_03_*.md and .bib (committed, ~14kB each) —

QUALITY BENCHMARK. Format / depth / structure to match or exceed.

- paper_prep/lit_review/topic_11_*.md and .bib (committed, ~14kB each) —

same — also a benchmark.

- SYNTHESIS.md, CHRONOLOGY.md, GAPS.md from a partial earlier synthesis run

(built from incomplete substrate; will be regenerated by the synth task).

- prior wg log entries showing codex agents bailing in 30-60s — that is

the failure mode you must NOT repeat.

You are claude:sonnet. The task is a literature review with web search +

1500-3000 words of prose + 10-30 BibTeX entries. Take the time to do the

work properly. The mandatory step-ordered preamble above this note still

applies (if the original preamble is present). If your topic does not have

the strict-step preamble (topic-03 and topic-11-2 retained their original

prompts), follow the same shape as those benchmark files.

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Required by

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